Methodologies for Transcript Profiling Using Long-Read Technologies (Q98177814)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:32733532%20AND%20SRC:MED&resulttype=core&format=json

9 August 2020

title

Methodologies for Transcript Profiling Using Long-Read Technologies (English)

1 reference

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9 August 2020

author name string

Spyros Oikonomopoulos

1 reference

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9 August 2020

Anthony Bayega

1 reference

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9 August 2020

Somayyeh Fahiminiya

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:32733532%20AND%20SRC:MED&resulttype=core&format=json

9 August 2020

Haig Djambazian

1 reference

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9 August 2020

Pierre Berube

1 reference

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9 August 2020

Jiannis Ragoussis

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9 August 2020

publication date

7 July 2020

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9 August 2020

published in

Frontiers in Genetics

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9 August 2020

volume

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9 August 2020

page(s)

606

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Creative Commons Attribution 4.0 International

9 August 2020

start time

7 July 2020

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

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Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

10 February 2021

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De novo clustering of long reads by gene from transcriptomics data

10 February 2021

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Direct RNA Sequencing of the Coding Complete Influenza A Virus Genome

10 February 2021

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Transcriptional fates of human-specific segmental duplications in brain

10 February 2021

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SMRT-Cappable-seq reveals complex operon variants in bacteria

10 February 2021

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Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA

10 February 2021

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Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq

10 February 2021

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From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy

10 February 2021

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Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

10 February 2021

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IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing.

10 February 2021

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Third-generation Sequencing Reveals Extensive Polycistronism and Transcriptional Overlapping in a Baculovirus.

10 February 2021

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Immune Modulation by Human Secreted RNases at the Extracellular Space.

10 February 2021

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Current and Future Methods for mRNA Analysis: A Drive Toward Single Molecule Sequencing

10 February 2021

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Transcript Profiling Using Long-Read Sequencing Technologies

10 February 2021

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Minimap2: pairwise alignment for nucleotide sequences

10 February 2021

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Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations.

10 February 2021

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Ribothrypsis, a novel process of canonical mRNA decay, mediates ribosome-phased mRNA endonucleolysis.

10 February 2021

1 reference

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Native RNA-Sequencing Throws its Hat into the Transcriptomics Ring.

10 February 2021

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Systematic comparison of small RNA library preparation protocols for next-generation sequencing.

10 February 2021

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Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

10 February 2021

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Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes

10 February 2021

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Highly parallel direct RNA sequencing on an array of nanopores.

10 February 2021

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Nanopore DNA Sequencing and Genome Assembly on the International Space Station.

10 February 2021

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Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome

10 February 2021

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Evaluation of tools for long read RNA-seq splice-aware alignment

10 February 2021

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Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing Events

10 February 2021

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Length-independent DNA packing into nanopore zero-mode waveguides for low-input DNA sequencing

10 February 2021

1 reference

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Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis.

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis.

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells.

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

ConcatSeq: A method for increasing throughput of single molecule sequencing by concatenating short DNA fragments.

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

10 February 2021

1 reference

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Charting the unknown epitranscriptome

10 February 2021

1 reference

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A reference human genome dataset of the BGISEQ-500 sequencer.

10 February 2021

1 reference

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Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

10 February 2021

1 reference

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On the design and prospects of direct RNA sequencing

10 February 2021

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Detecting DNA cytosine methylation using nanopore sequencing.

10 February 2021

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Single-cell mRNA isoform diversity in the mouse brain

10 February 2021

1 reference

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The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

10 February 2021

1 reference

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Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations

10 February 2021

1 reference

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Globin mRNA reduction for whole-blood transcriptome sequencing

10 February 2021

1 reference

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INC-Seq: accurate single molecule reads using nanopore sequencing

10 February 2021

1 reference

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A survey of the sorghum transcriptome using single-molecule long reads

10 February 2021

1 reference

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cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing.

10 February 2021

1 reference

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Coming of age: ten years of next-generation sequencing technologies

10 February 2021

1 reference

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Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II.

10 February 2021

1 reference

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Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

PacBio Sequencing and Its Applications

10 February 2021

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Global analysis of RNA cleavage by 5'-hydroxyl RNA sequencing.

10 February 2021

1 reference

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Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events

10 February 2021

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Structural insights into catalysis and dimerization enhanced exonuclease activity of RNase J.

10 February 2021

1 reference

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Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Successful test launch for nanopore sequencing

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Messenger RNA degradation in bacterial cells

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Many BCR-ABL1 compound mutations reported in chronic myeloid leukemia patients may actually be artifacts due to PCR-mediated recombination.

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

IVT-seq reveals extreme bias in RNA sequencing

10 February 2021

1 reference

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Defining a personal, allele-specific, and single-molecule long-read transcriptome

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

HIV-1 interacts with human endogenous retrovirus K (HML-2) envelopes derived from human primary lymphocytes

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs.

10 February 2021

1 reference

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Sequencing depth and coverage: key considerations in genomic analyses

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Base preferences in non-templated nucleotide incorporation by MMLV-derived reverse transcriptases

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Full-length RNA-seq from single cells using Smart-seq2.

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Quantitative single-cell RNA-seq with unique molecular identifiers

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Characterization of the human ESC transcriptome by hybrid sequencing

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Assessment of transcript reconstruction methods for RNA-seq

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Systematic evaluation of spliced alignment programs for RNA-seq data

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

A single-molecule long-read survey of the human transcriptome

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Smart-seq2 for sensitive full-length transcriptome profiling in single cells.

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Cloning full-length transcripts and transcript variants using 5' and 3' RACE.

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Sequencing the unsequenceable: expanded CGG-repeat alleles of the fragile X gene

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

GENCODE: the reference human genome annotation for The ENCODE Project

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Landscape of transcription in human cells

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Regulation of cytoplasmic mRNA decay

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Bovine pancreatic ribonuclease: fifty years of the first enzymatic reaction mechanism

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Optimization of enzymatic reaction conditions for generating representative pools of cDNA from small RNA.

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

T2 Family ribonucleases: ancient enzymes with diverse roles

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

10 February 2021

Direct RNA sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications.

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Small silencing RNAs: an expanding universe

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Real-time DNA sequencing from single polymerase molecules

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Efficient 5' cap-dependent RNA purification : use in identifying and studying subsets of RNA.

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Potential pitfalls in the accuracy of analysis of natural sense-antisense RNA pairs by reverse transcription-PCR

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Escherichia coli DNA polymerase III epsilon subunit increases Moloney murine leukemia virus reverse transcriptase fidelity and accuracy of RT-PCR procedures

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Error propagation in relative real-time reverse transcription polymerase chain reaction quantification models: the balance between accuracy and precision.

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

The complexity of the mammalian transcriptome

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Reverse transcriptase template switching and false alternative transcripts.

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Understanding alternative splicing: towards a cellular code

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

GMAP: a genomic mapping and alignment program for mRNA and EST sequences

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Full-Length cDNA Synthesis for Long-Distance RT-PCR of Large mRNA Transcripts

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Mechanisms of alternative pre-messenger RNA splicing

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

mRNA decay in Escherichia coli comes of age.

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

The complete gene sequence of titin, expression of an unusual approximately 700-kDa titin isoform, and its interaction with obscurin identify a novel Z-line to I-band linking system

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

DNA synthesis fidelity by the reverse transcriptase of the yeast retrotransposon Ty1.

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

CapSelect: a highly sensitive method for 5' CAP-dependent enrichment of full-length cDNA in PCR-mediated analysis of mRNAs.

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

The transmembrane kinase Ire1p is a site-specific endonuclease that initiates mRNA splicing in the unfolded protein response

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

The yeast tRNA splicing endonuclease: a tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

Reverse transcription and DNA amplification by a Thermus thermophilus DNA polymerase

10 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=7358353

10 February 2021

Identifiers

DOI

10.3389/FGENE.2020.00606

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:32733532%20AND%20SRC:MED&resulttype=core&format=json

9 August 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:32733532%20AND%20SRC:MED&resulttype=core&format=json

9 August 2020

PubMed publication ID

32733532

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:32733532%20AND%20SRC:MED&resulttype=core&format=json